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Batch 1: Updates for paper, SE grid compatibility, bug fixes #27

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merged 5 commits into from
Nov 2, 2023
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Merged

Batch 1: Updates for paper, SE grid compatibility, bug fixes #27

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7f1d099
Updates for paper, SE grid compatibility, bug fixes
jimmielin Oct 17, 2023
a66be15
Slight formatting updates to GEOS-Chem run log output
jimmielin Oct 19, 2023
972c057
Update GEOS-Chem external tag to 14.1.2
jimmielin Oct 20, 2023
cf0e7b6
Update Externals_CAM.cfg to use hash as 14.1.2 matches branch as well
jimmielin Oct 30, 2023
95cd2a5
Revert "Update Externals_CAM.cfg to use hash as 14.1.2 matches branch…
jimmielin Oct 30, 2023
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2 changes: 1 addition & 1 deletion Externals_CAM.cfg
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Original file line number Diff line number Diff line change
Expand Up @@ -80,7 +80,7 @@ required = True
local_path = src/chemistry/geoschem/geoschem_src
protocol = git
repo_url = https://github.com/geoschem/geos-chem.git
tag = 14.1.1
tag = 14.1.2
required = True

[hemco]
Expand Down
92 changes: 60 additions & 32 deletions src/chemistry/geoschem/chemistry.F90
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Expand Up @@ -656,6 +656,8 @@ subroutine chem_readnl(nlfile)
use aero_model, only : aero_model_readnl
use dust_model, only : dust_readnl
#endif
! For dry deposition on unstructured grids
use mo_drydep, only : drydep_srf_file

! args
CHARACTER(LEN=*), INTENT(IN) :: nlfile ! filepath for file containing namelist input
Expand All @@ -672,9 +674,9 @@ subroutine chem_readnl(nlfile)
RC = GC_SUCCESS

namelist /chem_inparm/ depvel_lnd_file
namelist /chem_inparm/ drydep_srf_file

! ghg chem

namelist /chem_inparm/ bndtvg, h2orates, ghg_chem

if (debug .and. masterproc) write(iulog,'(a)') 'chem_readnl: reading namelists for GEOS-Chem chemistry'
Expand Down Expand Up @@ -831,7 +833,7 @@ subroutine chem_readnl(nlfile)
IF (IERR == 0) THEN
READ(unitn, chem_inparm, IOSTAT=IERR)
IF (IERR /= 0) THEN
CALL endrun('chem_readnl: ERROR reading namelist')
CALL endrun('chem_readnl: ERROR reading namelist chem_inparm')
ENDIF
ENDIF
CLOSE(unitn)
Expand Down Expand Up @@ -864,6 +866,10 @@ subroutine chem_readnl(nlfile)
IF ( ierr /= mpi_success ) then
CALL endrun(subname//': MPI_BCAST ERROR: depvel_lnd_file')
ENDIF
CALL mpi_bcast(drydep_srf_file, LEN(drydep_srf_file), mpi_character, masterprocid, mpicom, ierr)
IF ( ierr /= mpi_success ) then
CALL endrun(subname//': MPI_BCAST ERROR: drydep_srf_file')
ENDIF
CALL mpi_bcast(ghg_chem, 1, mpi_logical, masterprocid, mpicom, ierr)
IF ( ierr /= mpi_success ) then
CALL endrun(subname//': MPI_BCAST ERROR: ghg_chem')
Expand Down Expand Up @@ -1122,32 +1128,31 @@ subroutine chem_init(phys_state, pbuf2d)
Input_Opt%thisCPU = myCPU
Input_Opt%amIRoot = MasterProc

!IF ( MasterProc ) THEN
IF ( .True. ) THEN
CALL Read_Input_File( Input_Opt = Input_Opt, &
State_Grid = maxGrid, &
RC = RC )

! First setup directories
Input_Opt%Chem_Inputs_Dir = TRIM(geoschem_cheminputs)
Input_Opt%SpcDatabaseFile = TRIM(speciesDB)
Input_Opt%FAST_JX_DIR = TRIM(geoschem_cheminputs)//'FAST_JX/v2020-02/'
CALL Read_Input_File( Input_Opt = Input_Opt, &
State_Grid = maxGrid, &
RC = RC )

!----------------------------------------------------------
! CESM-specific input flags
!----------------------------------------------------------

! onlineAlbedo -> True (use CLM albedo)
! -> False (read monthly-mean albedo from HEMCO)
Input_Opt%onlineAlbedo = .true.
! First setup directories
Input_Opt%Chem_Inputs_Dir = TRIM(geoschem_cheminputs)
Input_Opt%SpcDatabaseFile = TRIM(speciesDB)
Input_Opt%FAST_JX_DIR = TRIM(geoschem_cheminputs)//'FAST_JX/v2020-02/'

!----------------------------------------------------------
! CESM-specific input flags
!----------------------------------------------------------

! applyQtend: apply tendencies of water vapor to specific humidity
Input_Opt%applyQtend = .False.
! onlineAlbedo -> True (use CLM albedo)
! -> False (read monthly-mean albedo from HEMCO)
Input_Opt%onlineAlbedo = .true.

IF ( .NOT. Input_Opt%LSOA ) THEN
CALL ENDRUN('CESM2-GC requires the complex SOA option to be on!')
ENDIF
! applyQtend: apply tendencies of water vapor to specific humidity
Input_Opt%applyQtend = .False.

! correctConvUTLS: Apply photolytic correction for convective scavenging of soluble tracers?
Input_Opt%correctConvUTLS = .true.

IF ( .NOT. Input_Opt%LSOA ) THEN
CALL ENDRUN('CESM2-GC requires the complex SOA option to be on!')
ENDIF

CALL Validate_Directories( Input_Opt, RC )
Expand Down Expand Up @@ -1482,7 +1487,7 @@ subroutine chem_init(phys_state, pbuf2d)
CALL aero_model_init( pbuf2d )

! Initialize drydep
CALL drydep_inti( depvel_lnd_file)
CALL drydep_inti( depvel_lnd_file )
#endif

IF ( gas_wetdep_method == 'NEU' ) THEN
Expand Down Expand Up @@ -1592,6 +1597,18 @@ subroutine chem_init(phys_state, pbuf2d)
State_Chm = State_Chm(I), &
State_Diag = State_Diag(I), &
State_Grid = State_Grid(I) )

! Because not all CPUs in the communicator have the same amount of chunks,
! it is only guaranteed that the first chunk in all CPUs can participate in
! MPI_bcast of the NOXCOEFF array. So only the root CPU & root chunk will
! read the NOXCOEFF array from disk, then broadcast to all other CPU's first
! chunks, then remaining chunks can be copied locally without MPI. (hplin, 10/17/23)
IF( I == BEGCHUNK ) THEN
CALL mpi_bcast( State_Chm(I)%NOXCOEFF, size(State_Chm(I)%NOXCOEFF), mpi_real8, masterprocid, mpicom, ierr )
IF ( ierr /= mpi_success ) CALL endrun('Error in mpi_bcast of NOXCOEFF in first chunk')
ELSE
State_CHM(I)%NOXCOEFF = State_Chm(BEGCHUNK)%NOXCOEFF
ENDIF
ENDDO
ENDIF

Expand Down Expand Up @@ -1673,7 +1690,7 @@ subroutine chem_init(phys_state, pbuf2d)
! Cleanup
Call Cleanup_State_Grid( maxGrid, RC )

if (debug .and. masterproc) write(iulog,'(a)') 'chem_init: GEOS-Chem chemistry initialization complete'
if (masterproc) write(iulog,'(a)') 'chem_init: GEOS-Chem chemistry initialization complete'

end subroutine chem_init

Expand Down Expand Up @@ -2180,6 +2197,12 @@ subroutine chem_timestep_tend( state, ptend, cam_in, cam_out, dT, pbuf, fh2o )
ENDDO

#if defined( MODAL_AERO )
! NOTE: GEOS-Chem bulk aerosol concentrations (BCPI, BCPO, SO4, ...) are ZEROED OUT
! here in order to be reconstructed from the modal concentrations.
!
! This means that any changes to the BULK mass will be ignored between the end
! of the gas_phase_chemdr and the beginning of the next!!
!
! First reset State_Chm%Species to zero out MAM-inherited GEOS-Chem aerosols
DO M = 1, ntot_amode
DO SM = 1, nspec_amode(M)
Expand Down Expand Up @@ -2227,7 +2250,8 @@ subroutine chem_timestep_tend( state, ptend, cam_in, cam_out, dT, pbuf, fh2o )
! map2GC(bulk constituent index) constituent index (bulk) GEOS-Chem species index (bulk)
! map2MAM4(SM, M) SM, M (modal) constituent index (bulk)
! (map2MAM4 is a N to 1 operation)
!
! Query functions:
! xname_massptr(SM, M) SM, M NAME of modal aer (bc_a1, bc_a4, ...)
!------------------------------------------------------------------------------------------
binRatio = 0.0e+00_r8
DO M = 1, ntot_amode
Expand Down Expand Up @@ -2405,15 +2429,18 @@ subroutine chem_timestep_tend( state, ptend, cam_in, cam_out, dT, pbuf, fh2o )
ENDIF
#endif

! Convert mass fluxes to VMR as needed for MAM4 aerosols (these operate on vmr0 - initial and vmr1 - end of timestep)
DO N = 1, gas_pcnst
! See definition of map2chm
M = map2chm(N)
IF ( M > 0 ) THEN
! Is a GEOS-Chem species?
vmr0(:nY,:nZ,N) = State_Chm(LCHNK)%Species(M)%Conc(1,:nY,nZ:1:-1) * &
MWDry / adv_mass(N)
! We'll substract concentrations after chemistry later
mmr_tend(:nY,:nZ,N) = REAL(State_Chm(LCHNK)%Species(M)%Conc(1,:nY,nZ:1:-1),r8)
ELSEIF ( M < 0 ) THEN
! Is a MAM4 species? Get VMR from state%q directly.
vmr0(:nY,:nZ,N) = state%q(:nY,:nZ,-M) * &
MWDry / adv_mass(N)
mmr_tend(:nY,:nZ,N) = state%q(:nY,:nZ,-M)
Expand Down Expand Up @@ -3865,6 +3892,8 @@ subroutine chem_timestep_tend( state, ptend, cam_in, cam_out, dT, pbuf, fh2o )

! Deal with aerosol SOA species
! First deal with lowest two volatility bins
! Only map TOSA0 (K1) and ASOAN (K2) to soa1_ and soa2_, according to Fritz et al.
! SOAIE (K3) and SOAGX (K4) were mapped in the code but are inconsistent with the model description paper.
speciesName_1 = 'TSOA0'
speciesName_2 = 'ASOAN'
speciesName_3 = 'SOAIE'
Expand All @@ -3886,10 +3915,9 @@ subroutine chem_timestep_tend( state, ptend, cam_in, cam_out, dT, pbuf, fh2o )
N = lptr2_soa_a_amode(M,iBin)
IF ( N <= 0 ) CYCLE
P = mapCnst(N)
IF ( P > 0 .AND. K1 > 0 .AND. K2 > 0 .AND. K3 > 0 .AND. K4 > 0 ) THEN
IF ( P > 0 .AND. K1 > 0 .AND. K2 > 0 ) THEN
vmr1(:nY,:nZ,P) = state%q(:nY,:nZ,N) / bulkMass(:nY,:nZ) &
* (vmr1(:nY,:nZ,K1) + vmr1(:nY,:nZ,K2) + &
vmr1(:nY,:nZ,K3) + vmr1(:nY,:nZ,K4))
* (vmr1(:nY,:nZ,K1) + vmr1(:nY,:nZ,K2))
ENDIF
ENDDO
ENDDO
Expand Down Expand Up @@ -4182,8 +4210,8 @@ subroutine chem_timestep_tend( state, ptend, cam_in, cam_out, dT, pbuf, fh2o )
Nullify(NEvapr )
Nullify(cmfdqr )

IF ( rootChunk ) WRITE(iulog,*) ' GEOS-Chem Chemistry step ', iStep, ' completed'
IF ( lastChunk ) WRITE(iulog,*) ' Chemistry completed on all chunks completed of MasterProc'
IF ( rootChunk ) WRITE(iulog,*) 'GEOS-Chem Chemistry step ', iStep, ' completed'
IF ( lastChunk ) WRITE(iulog,*) 'Chemistry completed on all chunks of root CPU'
IF ( FIRST ) THEN
FIRST = .false.
ENDIF
Expand Down